X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_tview_curses.c;fp=bam_tview_curses.c;h=571633c817b1e7a9fd899817c7972269898f5547;hb=3880f184334b2b5afe27de5c5a0f344cdcff1ef9;hp=0000000000000000000000000000000000000000;hpb=4773f0ea85f278fc544d762d707e92673232f1e4;p=samtools.git

diff --git a/bam_tview_curses.c b/bam_tview_curses.c
new file mode 100644
index 0000000..571633c
--- /dev/null
+++ b/bam_tview_curses.c
@@ -0,0 +1,234 @@
+#include "bam_tview_curses.h"
+
+
+
+
+static void curses_tv_destroy(tview_t* base)
+	{
+	curses_tview_t* tv=(curses_tview_t*)base;
+
+	
+	delwin(tv->wgoto); delwin(tv->whelp);
+	endwin();
+
+	base_tv_destroy(base);
+	
+	free(tv);
+	}
+
+curses_tview_t* curses_tv_init(const char *fn, const char *fn_fa, const char *samples)
+	{
+	curses_tview_t *tv = (curses_tview_t*)calloc(1, sizeof(curses_tview_t));
+	tview_t* base=(tview_t*)tv;
+	if(tv==0)
+		{
+		fprintf(stderr,"Calloc failed\n");
+		return 0;
+		}
+	
+	base_tv_init(base,fn,fn_fa,samples);
+	/* initialize callbacks */
+	base->destroy=curses_tv_destroy;
+	
+	initscr();
+	keypad(stdscr, TRUE);
+	clear();
+	noecho();
+	cbreak();
+	
+	getmaxyx(stdscr, base->mrow, base->mcol);
+	tv->wgoto = newwin(3, TV_MAX_GOTO + 10, 10, 5);
+	tv->whelp = newwin(29, 40, 5, 5);
+	
+	start_color();
+	init_pair(1, COLOR_BLUE, COLOR_BLACK);
+	init_pair(2, COLOR_GREEN, COLOR_BLACK);
+	init_pair(3, COLOR_YELLOW, COLOR_BLACK);
+	init_pair(4, COLOR_WHITE, COLOR_BLACK);
+	init_pair(5, COLOR_GREEN, COLOR_BLACK);
+	init_pair(6, COLOR_CYAN, COLOR_BLACK);
+	init_pair(7, COLOR_YELLOW, COLOR_BLACK);
+	init_pair(8, COLOR_RED, COLOR_BLACK);
+	init_pair(9, COLOR_BLUE, COLOR_BLACK);
+	return tv;
+	}
+
+
+static void tv_win_goto(curses_tview_t *tv, int *tid, int *pos)
+	{
+	char str[256], *p;
+	int i, l = 0;
+	tview_t *base=(tview_t*)tv;
+	wborder(tv->wgoto, '|', '|', '-', '-', '+', '+', '+', '+');
+	mvwprintw(tv->wgoto, 1, 2, "Goto: ");
+	for (;;) {
+		int c = wgetch(tv->wgoto);
+		wrefresh(tv->wgoto);
+		if (c == KEY_BACKSPACE || c == '\010' || c == '\177') {
+			if(l > 0) --l;
+		} else if (c == KEY_ENTER || c == '\012' || c == '\015') {
+			int _tid = -1, _beg, _end;
+			if (str[0] == '=') {
+				_beg = strtol(str+1, &p, 10) - 1;
+				if (_beg > 0) {
+					*pos = _beg;
+					return;
+				}
+			} else {
+				bam_parse_region(base->header, str, &_tid, &_beg, &_end);
+				if (_tid >= 0) {
+					*tid = _tid; *pos = _beg;
+					return;
+				}
+			}
+		} else if (isgraph(c)) {
+			if (l < TV_MAX_GOTO) str[l++] = c;
+		} else if (c == '\027') l = 0;
+		else if (c == '\033') return;
+		str[l] = '\0';
+		for (i = 0; i < TV_MAX_GOTO; ++i) mvwaddch(tv->wgoto, 1, 8 + i, ' ');
+		mvwprintw(tv->wgoto, 1, 8, "%s", str);
+	}
+}
+
+
+
+
+static void tv_win_help(curses_tview_t *tv) {
+	int r = 1;
+	tview_t* base=(tview_t*)base;
+	WINDOW *win = tv->whelp;
+	wborder(win, '|', '|', '-', '-', '+', '+', '+', '+');
+	mvwprintw(win, r++, 2, "        -=-    Help    -=- ");
+	r++;
+	mvwprintw(win, r++, 2, "?          This window");
+	mvwprintw(win, r++, 2, "Arrows     Small scroll movement");
+	mvwprintw(win, r++, 2, "h,j,k,l    Small scroll movement");
+	mvwprintw(win, r++, 2, "H,J,K,L    Large scroll movement");
+	mvwprintw(win, r++, 2, "ctrl-H     Scroll 1k left");
+	mvwprintw(win, r++, 2, "ctrl-L     Scroll 1k right");
+	mvwprintw(win, r++, 2, "space      Scroll one screen");
+	mvwprintw(win, r++, 2, "backspace  Scroll back one screen");
+	mvwprintw(win, r++, 2, "g          Go to specific location");
+	mvwprintw(win, r++, 2, "m          Color for mapping qual");
+	mvwprintw(win, r++, 2, "n          Color for nucleotide");
+	mvwprintw(win, r++, 2, "b          Color for base quality");
+	mvwprintw(win, r++, 2, "c          Color for cs color");
+	mvwprintw(win, r++, 2, "z          Color for cs qual");
+	mvwprintw(win, r++, 2, ".          Toggle on/off dot view");
+	mvwprintw(win, r++, 2, "s          Toggle on/off ref skip");
+	mvwprintw(win, r++, 2, "r          Toggle on/off rd name");
+	mvwprintw(win, r++, 2, "N          Turn on nt view");
+	mvwprintw(win, r++, 2, "C          Turn on cs view");
+	mvwprintw(win, r++, 2, "i          Toggle on/off ins");
+	mvwprintw(win, r++, 2, "q          Exit");
+	r++;
+	mvwprintw(win, r++, 2, "Underline:      Secondary or orphan");
+	mvwprintw(win, r++, 2, "Blue:    0-9    Green: 10-19");
+	mvwprintw(win, r++, 2, "Yellow: 20-29   White: >=30");
+	wrefresh(win);
+	wgetch(win);
+}
+
+void tv_loop(curses_tview_t *CTV)
+{
+	int tid, pos;
+	tview_t* tv=(tview_t*)CTV;
+	tid = tv->curr_tid; pos = tv->left_pos;
+	while (1) {
+		int c = getch();
+		switch (c) {
+			case '?': tv_win_help(CTV); break;
+			case '\033':
+			case 'q': goto end_loop;
+			case '/': 
+			case 'g': tv_win_goto(CTV, &tid, &pos); break;
+			case 'm': tv->color_for = TV_COLOR_MAPQ; break;
+			case 'b': tv->color_for = TV_COLOR_BASEQ; break;
+			case 'n': tv->color_for = TV_COLOR_NUCL; break;
+			case 'c': tv->color_for = TV_COLOR_COL; break;
+			case 'z': tv->color_for = TV_COLOR_COLQ; break;
+			case 's': tv->no_skip = !tv->no_skip; break;
+			case 'r': tv->show_name = !tv->show_name; break;
+			case KEY_LEFT:
+			case 'h': --pos; break;
+			case KEY_RIGHT:
+			case 'l': ++pos; break;
+			case KEY_SLEFT:
+			case 'H': pos -= 20; break;
+			case KEY_SRIGHT:
+			case 'L': pos += 20; break;
+			case '.': tv->is_dot = !tv->is_dot; break;
+			case 'N': tv->base_for = TV_BASE_NUCL; break;
+			case 'C': tv->base_for = TV_BASE_COLOR_SPACE; break;
+			case 'i': tv->ins = !tv->ins; break;
+			case '\010': pos -= 1000; break;
+			case '\014': pos += 1000; break;
+			case ' ': pos += tv->mcol; break;
+			case KEY_UP:
+			case 'j': --tv->row_shift; break;
+			case KEY_DOWN:
+			case 'k': ++tv->row_shift; break;
+			case KEY_BACKSPACE:
+			case '\177': pos -= tv->mcol; break;
+			case KEY_RESIZE: getmaxyx(stdscr, tv->mrow, tv->mcol); break;
+			default: continue;
+		}
+		if (pos < 0) pos = 0;
+		if (tv->row_shift < 0) tv->row_shift = 0;
+		tv_draw_aln(tv, tid, pos);
+	}
+end_loop:
+	return;
+}
+
+void error(const char *format, ...)
+{
+    if ( !format )
+    {
+        fprintf(stderr, "\n");
+        fprintf(stderr, "Usage: bamtk tview [options] <aln.bam> [ref.fasta]\n");
+        fprintf(stderr, "Options:\n");
+        fprintf(stderr, "   -p chr:pos      go directly to this position\n");
+        fprintf(stderr, "   -s STR          display only reads from this sample or grou\n");
+        fprintf(stderr, "\n\n");
+    }
+    else
+    {
+        va_list ap;
+        va_start(ap, format);
+        vfprintf(stderr, format, ap);
+        va_end(ap);
+    }
+    exit(-1);
+}
+
+
+int bam_tview_main(int argc, char *argv[])
+{
+	curses_tview_t *CTV;
+	tview_t* tv=NULL;
+    char *samples=NULL, *position=NULL;
+    int c;
+    while ((c = getopt(argc, argv, "s:p:")) >= 0) {
+        switch (c) {
+            case 's': samples=optarg; break;
+            case 'p': position=optarg; break;
+            default: error(NULL);
+        }
+    }
+	if (argc==optind) error(NULL);
+	CTV = curses_tv_init(argv[optind], (optind+1>=argc)? 0 : argv[optind+1], samples);
+	tv=(tview_t*)CTV;
+    if ( position )
+    {
+        int _tid = -1, _beg, _end;
+        bam_parse_region(tv->header, position, &_tid, &_beg, &_end);
+        if (_tid >= 0) { tv->curr_tid = _tid; tv->left_pos = _beg; }
+    }
+	tv_draw_aln(tv, tv->curr_tid, tv->left_pos);
+	tv_loop(CTV);
+	tv->destroy(tv);
+	free(tv);
+	return 0;
+}